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Sybilska E, Collin A, Sadat Haddadi B, Mur LAJ, Beckmann M, Guo W, Simpson CG, Daszkowska-Golec A. The cap-binding complex modulates ABA-responsive transcript splicing during germination in barley (Hordeum vulgare). Sci Rep 2024; 14:18278. [PMID: 39107424 PMCID: PMC11303550 DOI: 10.1038/s41598-024-69373-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024] Open
Abstract
To decipher the molecular bases governing seed germination, this study presents the pivotal role of the cap-binding complex (CBC), comprising CBP20 and CBP80, in modulating the inhibitory effects of abscisic acid (ABA) in barley. Using both single and double barley mutants in genes encoding the CBC, we revealed that the double mutant hvcbp20.ab/hvcbp80.b displays ABA insensitivity, in stark contrast to the hypersensitivity observed in single mutants during germination. Our comprehensive transcriptome and metabolome analysis not only identified significant alterations in gene expression and splicing patterns but also underscored the regulatory nexus among CBC, ABA, and brassinosteroid (BR) signaling pathways.
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Affiliation(s)
- Ewa Sybilska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Anna Collin
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | | | - Luis A J Mur
- Department of Life Science, Aberystwyth University, Aberystwyth, UK
| | - Manfred Beckmann
- Department of Life Science, Aberystwyth University, Aberystwyth, UK
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Craig G Simpson
- Cell and Molecular Sciences, James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland.
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Li H, Xia Y, Chen W, Chen Y, Cheng X, Chao H, Fan S, Jia H, Li M. An integrated QTL and RNA-seq analysis revealed new petal morphology loci in Brassica napus L. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:105. [PMID: 39026359 PMCID: PMC11264636 DOI: 10.1186/s13068-024-02551-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/05/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Rapeseed (Brassica napus L.) is one of the most important oil crops and a wildly cultivated horticultural crop. The petals of B. napus serve to protect the reproductive organs and attract pollinators and tourists. Understanding the genetic basis of petal morphology regulation is necessary for B. napus breeding. RESULTS In the present study, the quantitative trait locus (QTL) analysis for six B. napus petal morphology parameters in a double haploid (DH) population was conducted across six microenvironments. A total of 243 QTLs and five QTL hotspots were observed, including 232 novel QTLs and three novel QTL hotspots. The spatiotemporal transcriptomic analysis of the diversiform petals was also conducted, which indicated that the expression of plant hormone metabolic and cytoskeletal binding protein genes was variant among diversiform petals. CONCLUSIONS The integration of QTL and RNA-seq analysis revealed that plant hormones (including cytokinin, auxin, and gibberellin) and cytoskeleton were key regulators of the petal morphology. Subsequently, 61 high-confidence candidate genes of petal morphology regulation were identified, including Bn.SAUR10, Bn.ARF18, Bn.KIR1, Bn.NGA2, Bn.PRF1, and Bn.VLN4. The current study provided novel QTLs and candidate genes for further breeding B. napus varieties with diversiform petals.
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Affiliation(s)
- Huaixin Li
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yutian Xia
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wang Chen
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Yanru Chen
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Xin Cheng
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Hongbo Chao
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Shipeng Fan
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Haibo Jia
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Maoteng Li
- College of Life Science and Technology, Key Laboratory of Molecular Biophysics of the Ministry of Education, Huazhong University of Science and Technology, Wuhan, 430074, China.
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Wang X, Liu X, Song K, Du L. An insight into the roles of ubiquitin-specific proteases in plants: development and growth, morphogenesis, and stress response. FRONTIERS IN PLANT SCIENCE 2024; 15:1396634. [PMID: 38993940 PMCID: PMC11236618 DOI: 10.3389/fpls.2024.1396634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024]
Abstract
Ubiquitination is a highly conserved and dynamic post-translational modification in which protein substrates are modified by ubiquitin to influence their activity, localization, or stability. Deubiquitination enzymes (DUBs) counter ubiquitin signaling by removing ubiquitin from the substrates. Ubiquitin-specific proteases (UBPs), the largest subfamily of DUBs, are conserved in plants, serving diverse functions across various cellular processes, although members within the same group often exhibit functional redundancy. Here, we briefly review recent advances in understanding the biological roles of UBPs, particularly the molecular mechanism by which UBPs regulate plant development and growth, morphogenesis, and stress response, which sheds light on the mechanistic roles of deubiquitination in plants.
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Affiliation(s)
- Xiuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xuan Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kaixuan Song
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Yuan J, Li D, Liang Y, Meng Y, Li L, Yang L, Pei M, Feng L, Li J. An optimum study on the laser scanning confocal microscopy techniques for BiFC assay using plant protoplast. BOTANICAL STUDIES 2024; 65:2. [PMID: 38194078 PMCID: PMC10776556 DOI: 10.1186/s40529-024-00409-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/03/2024] [Indexed: 01/10/2024]
Abstract
BACKGROUND The bimolecular fluorescence complementation (BiFC) assay is commonly used for investigating protein-protein interactions. While several BiFC detection systems have been developed, there is a limited amount of research focused on using laser scanning confocal microscope (LSCM) techniques to observe protoplasts. Protoplasts are more susceptible to damage and instability compared to their original cell state due to the preparation treatments they undergo, which makes it challenging for researchers to manipulate them during observation under LSCMs. Therefore, it is crucial to utilize microscope techniques properly and efficiently in BiFC assays. RESULTS When the target fluorescence is weak, the autofluorescence of chloroplast particles in protoplasts can interfere with the detection of BiFC signals localized in the nuclear region. Spectrum analysis revealed that chloroplast autofluorescence can be excited by lasers of various types, with the highest fluorescence signal observed at around 660 nm. Furthermore, our investigation into the impact of different pipette tips on the integrity of protoplast samples indicated that the utilization of cut tips with larger openings can mitigate cell breakage. We presented a workflow of LSCM techniques for investigating protoplast BiFC and discussed the microscopic manipulation involved in sample preparation and image capturing. CONCLUSION When the BiFC signals are weak, they may be affected by chloroplast autofluorescence. However, when used properly, the autofluorescence of chloroplasts can serve as an excellent internal marker for effectively distinguishing other signals. In combination with other findings, this study can provide valuable reference for researchers conducting BiFC assays and related studies.
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Affiliation(s)
- Jinhong Yuan
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Daiyu Li
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yi Liang
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yao Meng
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Li Li
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Lin Yang
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Mingyue Pei
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Liuchun Feng
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Junhua Li
- Engineering Research Center of Crop Genetic Improvement and Germplasm Innovation in Henan Province, College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
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